The combustion of dual-fuel engines usually uses a pilot flame to burn out a background fuel inside a cylinder under high compression. The background fuel can be either a gaseous fuel or a volatile liquid fuel, commonly with low reactivity to prevent premature combustion and engine knocking; whereas the pilot flame is normally set off with the direct injection of a liquid fuel with adequate reactivity that is suitable for deterministic auto-ignition with a high compression ratio. In this work, directly injected butanol is used to generate the pilot flame, while intake port injected ethanol or butanol is employed as the background fuel. Compared with the conventional diesel-only combustion, dual-fuel operations not only broaden the fuel applicability, but also enhance the potential for clean combustion, in high efficiency engines. The amount of background fuel and the scheduling of pilot flame are investigated through extensive laboratory experiments. The early pilot injection, or multi-event pilot injection, is found effective to enact modulating the chemical reactivity of the fuel in the background; and conversely the background fuel to the pilot fuel in the foreground. Compared with the diesel injection as an ignition source, the butanol direct injection needs to be more precisely controlled for a successful ignition of the background fuel, due to butanol’s relatively lower reactivity to auto-ignition; however, the use of butanol is potentially promising for clean combustion in a compression ignition engine because the combustion generates low emissions of nitrogen oxidizes and smoke. Throughout the experiments, exhaust gas recirculation and intake air boost are applied to help reaching clean and efficient combustion.